It is best to add a little malt extract in at the beginning because research has shown a little greatly helps in extracting the oils from the hops. As long as the wort wasn't exposed to sources of infection like air while it was cooling you'll be fine. My first several batches I let cool overnight. fast cooling times help prevent bacteria from spreading before the yeast can get a foothold and help clarify your beer. More aesthetics, and there are easy ways to clarify later like chilling the beer for a week.

That doesn't sound right. You either mash a few pounds of grain 1sdt (partial mash),or add part of the malt,stir to dissolve. Then start hop additions & the timer. Sounds like you started with plain water?